At T+31 seconds in the launch of this Pioneer probe, the hydraulics system of the first stage of the booster developed a problem that eventually culminated in complete loss of pressure at T+213 seconds, only 4 seconds prior to main-engine cutoff of the first stage. Although second-stage performance was nominal, there was no way to compensate for the large pointing error introduced by the malfunctions in the first stage.

With the booster veering off course, ground control sent a command to destroy the vehicle at T+484 seconds. Pioneer-E was the last in a series of probes intended for studying interplanetary space from heliocentric orbit. An additional payload on the Thor-Delta L was a Test and Training Satellite (TETR) to test the Apollo ground tracking network.